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SarahAlidoostSarahAlidoost
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fix the bug in os environ and add opengl path
1 parent fc1807c commit cd79aa7

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Lines changed: 39 additions & 61 deletions

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‎notebooks/run_model_in_notebook.ipynb‎

Lines changed: 39 additions & 61 deletions
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 16,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 17,
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"metadata": {},
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"outputs": [
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{
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" 'DurationSize': '17520'}"
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]
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},
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"execution_count": 4,
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"execution_count": 17,
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 18,
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"metadata": {},
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"outputs": [
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{
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" 'DurationSize': '5'}"
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]
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},
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"execution_count": 5,
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"execution_count": 18,
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": 9,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 10,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Prepare work directory /home/sarah/temp/ecoextreml/input/NL-Hor_20220517_1102 for the station: NL-Hor\n",
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"Prepare work directory /home/sarah/temp/ecoextreml/input/ZA-Kru_20220517_1102 for the station: ZA-Kru\n"
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"Prepare work directory /home/sarah/temp/ecoextreml/input/NL-Hor_20220519_1455 for the station: NL-Hor\n",
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"Prepare work directory /home/sarah/temp/ecoextreml/input/ZA-Kru_20220519_1455 for the station: ZA-Kru\n"
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]
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}
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],
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},
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{
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"cell_type": "code",
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"execution_count": 20,
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"execution_count": 13,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/usr/local/MATLAB/MATLAB_Runtime/v910/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/extern/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/sys/opengl/lib/glnxa64\n"
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]
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}
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],
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"source": [
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"# # Set LD_LIBRARY_PATH\n",
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"# matlab_path = !whereis MATLAB\n",
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"# matlab_path = matlab_path.s.split(\": \")[1]\n",
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"# os.environ['LD_LIBRARY_PATH'] = f\"{matlab_path}/MATLAB_Runtime/v910/runtime/glnxa64:f{matlab_path}/MATLAB_Runtime/v910/bin/glnxa64:{matlab_path}/MATLAB_Runtime/v910/sys/os/glnxa64:{matlab_path}/MATLAB_Runtime/v910/extern/bin/glnxa64\""
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"matlab_path = !whereis MATLAB\n",
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"matlab_path = matlab_path.s.split(\": \")[1]\n",
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"os.environ['LD_LIBRARY_PATH'] = (\n",
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" f\"{matlab_path}/MATLAB_Runtime/v910/runtime/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/v910/bin/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/v910/sys/os/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/v910/extern/bin/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/v910/sys/opengl/lib/glnxa64\")\n",
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"print(os.environ['LD_LIBRARY_PATH'])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Run STEMMUS-SCOPE with the forcing: NL-Hor_2008-2011_FLUXNET2015_Met.nc\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n",
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"libGL error: failed to load driver: iris\n",
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"libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n",
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"libGL error: failed to load driver: iris\n",
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"libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n",
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"libGL error: failed to load driver: swrast\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reading config from /home/sarah/temp/ecoextreml/input/NL-Hor_20220517_1102/NL-Hor_20220517_1102_config.txt\n",
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"Run STEMMUS-SCOPE with the forcing: NL-Hor_2008-2011_FLUXNET2015_Met.nc\n",
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"Reading config from /home/sarah/temp/ecoextreml/input/NL-Hor_20220519_1455/NL-Hor_20220519_1455_config.txt\n",
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"\n",
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" The calculations start now \n",
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"Run STEMMUS-SCOPE with the forcing: ZA-Kru_2000-2002_FLUXNET2015_Met.nc\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n",
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"libGL error: failed to load driver: iris\n",
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"libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n",
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"libGL error: failed to load driver: iris\n",
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"libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)\n",
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"libGL error: failed to load driver: swrast\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reading config from /home/sarah/temp/ecoextreml/input/ZA-Kru_20220517_1102/ZA-Kru_20220517_1102_config.txt\n",
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"Run STEMMUS-SCOPE with the forcing: ZA-Kru_2000-2002_FLUXNET2015_Met.nc\n",
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"Reading config from /home/sarah/temp/ecoextreml/input/ZA-Kru_20220519_1455/ZA-Kru_20220519_1455_config.txt\n",
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"\n",
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" The calculations start now \n",
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" The calculations end now \r"
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/home/sarah/temp/ecoextreml/output/NL-Hor_2022-05-13-1436/ECdata.csv\n",
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"/home/sarah/temp/ecoextreml/output/NL-Hor_2022-05-19-1457/ECdata.csv\n",
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"Reading variable metadata from /home/sarah/GitHub/STEMMUS_SCOPE/utils/csv_to_nc/Variables_will_be_in_NetCDF_file.csv\n",
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"Creating /home/sarah/temp/ecoextreml/output/NL-Hor_2022-05-13-1436/NL-Hor_2022-05-13-1436_STEMMUS_SCOPE.nc \n",
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"Creating /home/sarah/temp/ecoextreml/output/NL-Hor_2022-05-19-1457/NL-Hor_2022-05-19-1457_STEMMUS_SCOPE.nc \n",
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"Reading data from file: radiation.csv\n",
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"Reading data from file: fluxes.csv\n",
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"Reading data from file: surftemp.csv\n",
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"Reading data from file: Sim_Temp.csv\n",
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"Reading data from file: Sim_Theta.csv\n",
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"Reading data from file: aerodyn.csv\n",
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"Reading data from file: ECdata.csv\n",
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"Done writing /home/sarah/temp/ecoextreml/output/NL-Hor_2022-05-13-1436/NL-Hor_2022-05-13-1436_STEMMUS_SCOPE.nc\n",
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"/home/sarah/temp/ecoextreml/output/ZA-Kru_2022-05-13-1436/ECdata.csv\n",
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"Done writing /home/sarah/temp/ecoextreml/output/NL-Hor_2022-05-19-1457/NL-Hor_2022-05-19-1457_STEMMUS_SCOPE.nc\n",
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"/home/sarah/temp/ecoextreml/output/ZA-Kru_2022-05-19-1458/ECdata.csv\n",
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"Reading variable metadata from /home/sarah/GitHub/STEMMUS_SCOPE/utils/csv_to_nc/Variables_will_be_in_NetCDF_file.csv\n",
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"Creating /home/sarah/temp/ecoextreml/output/ZA-Kru_2022-05-13-1436/ZA-Kru_2022-05-13-1436_STEMMUS_SCOPE.nc \n",
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"Creating /home/sarah/temp/ecoextreml/output/ZA-Kru_2022-05-19-1458/ZA-Kru_2022-05-19-1458_STEMMUS_SCOPE.nc \n",
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"Reading data from file: radiation.csv\n",
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"Reading data from file: fluxes.csv\n",
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"Reading data from file: surftemp.csv\n",
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"Reading data from file: Sim_Temp.csv\n",
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"Reading data from file: Sim_Theta.csv\n",
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"Reading data from file: aerodyn.csv\n",
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"Reading data from file: ECdata.csv\n",
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"Done writing /home/sarah/temp/ecoextreml/output/ZA-Kru_2022-05-13-1436/ZA-Kru_2022-05-13-1436_STEMMUS_SCOPE.nc\n"
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"Done writing /home/sarah/temp/ecoextreml/output/ZA-Kru_2022-05-19-1458/ZA-Kru_2022-05-19-1458_STEMMUS_SCOPE.nc\n"
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]
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}
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],

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